Having rewatched both recently, BB being the first time in a year, I can safely say it is TDKR. It may have flaws, but it leaves so much more to chew on in terms of story, themes, and characters beyond Bruce Wayne. Bruce's best movie is BB, but it is so formulaic in comparison to the sequels. TDKR is unlike any other superhero movie ever made and for that I am thankful. Plus characters like BAne and Selina Kyle just put Rachel Dawes, Scarecrow, etc. to shame. And TDKR has a great third act.

So that is my vote.

__________________
"Let us disappoint the Men who are raising themselves upon the ruin of this Country."